Three different morphologies can occur at the interface of inorganic and polymeric phases in mixed matrix membranes (MMMs). These morphologies are characterized by their different parameters such as partial pore blockage factor (α), polymer chain rigidification factor (β), and thickness of rigidified layer or void region. In this study, the morphology of three MMMs has been evaluated using a comprehensive computational method. The average absolute relative error (%AARE) is used as a criterion for optimizing three various MMM morphological parameters. According to the obtained optimum parameters, it was confirmed that two MMMs of C60/Matrimid and PVAc-Zeolite 4A have pore blockage and polymer chain rigidified defects. The results show that the morphology of ZIF-8/6FDA-DAM can be considered as an ideal morphology. After obtaining the morphological parameters, the permeability of the studied MMMs was predicted based on the modified Maxwell model and good agreement was observed between the calculated value and the experimental data.